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- PDB-8is2: Crystal structure of a polyketide aromatase/cyclase Abx(+)D from ... -

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Basic information

Entry
Database: PDB / ID: 8is2
TitleCrystal structure of a polyketide aromatase/cyclase Abx(+)D from Actinomycetes sp. MA7150.
ComponentsCyclase
KeywordsBIOSYNTHETIC PROTEIN / aromatase / cyclase / polyketide
Function / homologyPolyketide synthesis cyclase / Polyketide synthesis cyclase superfamily / Polyketide synthesis cyclase / polyketide biosynthetic process / Dimeric alpha-beta barrel / Cyclase
Function and homology information
Biological speciesuncultured actinomycete (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsLuo, S. / Chen, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: An unusual aromatase/cyclase programs the formation of the phenyldimethylanthrone framework in anthrabenzoxocinones and fasamycin.
Authors: Jiang, K. / Chen, X. / Yan, X. / Li, G. / Lin, Z. / Deng, Z. / Luo, S. / Qu, X.
History
DepositionMar 20, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclase
B: Cyclase


Theoretical massNumber of molelcules
Total (without water)26,8802
Polymers26,8802
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-19 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.945, 50.945, 74.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Cyclase / polyketide aromatase/cyclase Abx(+)D


Mass: 13440.099 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence reference for Actinomycetes sp. MA7150 is not available at the time of biocuration. Current reference is A0A2U3TEK9.
Source: (gene. exp.) uncultured actinomycete (environmental samples)
Gene: abxD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U3TEK9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.78 %
Crystal growTemperature: 293.15 K / Method: liquid diffusion / pH: 8.1 / Details: 0.25 M Hepes, 60% Tacsimate, 0.17 M NDSB-211

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979191 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 1.32→38 Å / Num. obs: 49575 / % possible obs: 97.5 % / Redundancy: 2.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Net I/σ(I): 9.2
Reflection shellResolution: 1.32→1.39 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 7369 / CC1/2: 0.765 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→21.05 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 35.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2753 2404 4.85 %
Rwork0.224 --
obs0.2265 49536 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→21.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 0 152 1829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051716
X-RAY DIFFRACTIONf_angle_d0.7542322
X-RAY DIFFRACTIONf_dihedral_angle_d14.009639
X-RAY DIFFRACTIONf_chiral_restr0.075253
X-RAY DIFFRACTIONf_plane_restr0.007300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.350.31041690.29382823X-RAY DIFFRACTION99
1.35-1.380.31811260.27492872X-RAY DIFFRACTION99
1.38-1.410.29741320.26172767X-RAY DIFFRACTION99
1.41-1.450.31541130.25952831X-RAY DIFFRACTION99
1.45-1.480.28811640.26042792X-RAY DIFFRACTION98
1.48-1.530.32221410.23642784X-RAY DIFFRACTION98
1.53-1.580.26791550.23492763X-RAY DIFFRACTION98
1.58-1.630.31931200.26312810X-RAY DIFFRACTION98
1.63-1.70.31861510.25272814X-RAY DIFFRACTION98
1.7-1.780.32231240.22122778X-RAY DIFFRACTION98
1.78-1.870.28151530.26412773X-RAY DIFFRACTION98
1.87-1.990.2651530.25782710X-RAY DIFFRACTION97
1.99-2.140.26861620.23542755X-RAY DIFFRACTION96
2.14-2.360.30471360.23442664X-RAY DIFFRACTION95
2.36-2.70.2731410.24212749X-RAY DIFFRACTION96
2.7-3.390.25311220.21362777X-RAY DIFFRACTION97
3.4-21.050.26481420.19082670X-RAY DIFFRACTION95

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